Thanks very much, M4H35H. That was a very helpful suggestion! PDF-XChange Viewer works beautifully, although the 'flatten comments' function requires a pro license if you want to save the flattened file (which I will need to do for some files).
However, your post also helped me to find a solution in Acrobat Pro (which I already have via work). The built-in 'flatten comments' function in Acrobat Pro's 'preflight' menu does not work well at all well - around 60% of the pen strokes simply disappear. However, running the following command in Acrobat Pro's interactive javascript console flattened all the comments correctly.
Code:
this.flattenPages();
The resulting PDF prints perfectly.
For a FOSS solution, I assume ghostscript can be used to do this. I'll give it a try on my Linux machine at home this weekend.
But anyway, thanks very much. That's resolved my problem.